RetrogeneDB ID: retro_mmul_761

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099548049510:24139..25164(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GALM
• Ensembl ID: ENSMMUG00000008248
• Aliases: None
• Description: galactose mutarotase (aldose 1-epimerase) [Source:HGNC Symbol;Acc:24063]

Sequence

>retro_mmul_761
ATGGCTTCGGTGACCAGAGCCGTGTTTGGAGAGCTGCCCTTGGGAGGAGGGACAATGGAAAAGTTCCAGCTGCAGTCAGA
CCTCCTGAGAGTGGACATCATCTCCTGGGGCTGCACGATCACAGCCCTAGAGGTCAAAGACAGGCAGGGGAGAGCCTCAG
AGGTGGTGCTTGGCTTCACCGAGTTGGAAGGATACCTCCAAAAGCAGCCATACTTTGGAGCAGTTATTGGGAGGGTGGAC
AACTGAATCGCCAAAGGAACCTTCAAGGTGGATGGGAAGGAGTATCACCTGGCCATTAACAAGGAACCCAACAGTCTGCA
TGGAGGAGTCAGAGGGTTTGATAAGGTGCTCTGGACCCCTCGGGTGCTGTCCAATGGCGTCCCGTTTTCGCGCGTCAGTC
CAGATGGTGAGGAAGGCTACCCCCGAGAGTTAAAAGTCTGGGTGACATACACCCTGGATGGCGGGGAGCTCGTGGTCAAC
TATAGAGCACAGGCCAGTCAGGCCACACCAGTCAACCTGACCAACCATTCTTACTTCAACCTGCAGGCCAGGGTTCCCCG
AATATATATGACCATGAAGTCACCATAGAAGCGGATACTTACTTGCCTGCGGATGAAACCCTGATTCCTATAGGAGAAGT
TGCCCCGGTGCAAGGAACTGCATTCGACCTGAGAAAGCCAGTGGAGCTGGGAAAACACCTGCAGGACTTCCATCTCAATG
GTTTTGACCACAATTTCTGTCTGAAGGGATCGAAAGAAAAGCATCTTTGTGCAAGGGTGCATCATGCTGCAAGCGGGCGG
GTACTAGAAGTATACACCACCCAGCCCGGGGTCCAGTTCTACACGGGCAACTTCCTGGATGGCACATTAAAGGGCAAGAA
TGGAGCTGTCTATCCCAAGCACTCTGGTTTCTGCCTGGAGACTCAGAACTGGCCTGACGCAGTCAATCAGCCCCACTTCC
CTCCTGTGCTGCTGAGGCCTGGGGAGGAGTATGACCACACCACCTGGTTCAAGTTTTCTGTGGCT

Alignment

ORF - retro_mmul_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASVTRAAFGELPSGGGTVEKFQLQSDLLRVDIISWGCTITALEVKDRQGRASDVVLGFAELEGYLQKQP
          MASVTRA.FGELP.GGGT.EKFQLQSDLLRVDIISWGCTITALEVKDRQGRAS.VVLGF.ELEGYLQKQP
Retrocopy MASVTRAVFGELPLGGGTMEKFQLQSDLLRVDIISWGCTITALEVKDRQGRASEVVLGFTELEGYLQKQP

Parental  YFGAVIGRVANRIAKGTFKVDGKEYHLAINKEPNSLHGGVRGFDKVLWTPRVLSNGVQFSRISPDGEEGY
          YFGAVIGRV.N.IAKGTFKVDGKEYHLAINKEPNSLHGGVRGFDKVLWTPRVLSNGV.FSR.SPDGEEGY
Retrocopy YFGAVIGRVDN*IAKGTFKVDGKEYHLAINKEPNSLHGGVRGFDKVLWTPRVLSNGVPFSRVSPDGEEGY

Parental  PGELKVWVTYTLDGGELVVNYRAQASQATPVNLTNHSYFNL-AGQGSPNIYDHEVTIEADTYLPVDETLI
          P.ELKVWVTYTLDGGELVVNYRAQASQATPVNLTNHSYFNL.AGQGSPNIYDHEVTIEADTYLP.DETLI
Retrocopy PRELKVWVTYTLDGGELVVNYRAQASQATPVNLTNHSYFNL<AGQGSPNIYDHEVTIEADTYLPADETLI

Parental  PIGEVAPVQGTAFDLRKPVELGKHLQDFHLNGFDHNFCLKGSKEKHFCARVHHAASGRVLEVYTTQPGVQ
          PIGEVAPVQGTAFDLRKPVELGKHLQDFHLNGFDHNFCLKGSKEKH.CARVHHAASGRVLEVYTTQPGVQ
Retrocopy PIGEVAPVQGTAFDLRKPVELGKHLQDFHLNGFDHNFCLKGSKEKHLCARVHHAASGRVLEVYTTQPGVQ

Parental  FYTGNFLDGTLKGKNGAIYPKHSGFCLETQNWPDAVNQPHFPPVLLRPGEEYDHTTWFKFSVA
          FYTGNFLDGTLKGKNGA.YPKHSGFCLETQNWPDAVNQPHFPPVLLRPGEEYDHTTWFKFSVA
Retrocopy FYTGNFLDGTLKGKNGAVYPKHSGFCLETQNWPDAVNQPHFPPVLLRPGEEYDHTTWFKFSVA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.11 RPM	1.79 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.13 RPM
SRP007412_cerebellum	0.00 RPM	2.32 RPM
SRP007412_heart	0.06 RPM	13.13 RPM
SRP007412_kidney	1.06 RPM	114.20 RPM
SRP007412_liver	0.28 RPM	64.01 RPM
SRP007412_testis	0.00 RPM	4.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_761 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_761 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015006	1 retrocopy	retro_meug_2094,
Macaca mulatta	ENSMMUG00000008248	1 retrocopy	retro_mmul_761 ,
Oryctolagus cuniculus	ENSOCUG00000006325	1 retrocopy	retro_ocun_1151,
Sus scrofa	ENSSSCG00000008486	1 retrocopy	retro_sscr_147,
Tupaia belangeri	ENSTBEG00000003695	2 retrocopies	retro_tbel_2040, retro_tbel_2771,